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CRA_Updated_Version/CRA_Toolbox_GUI/ReadMe.txt

+#################################
+# Files description
+#################################
+
+### BEFORE RUNNING THE TOOLBOX, THE USER MUST HAD TO THE PATH THE FOLDER CLASSES AND THE FOLDER EXAMPLES WHERE THE MODELS ARE SAVED ###
+
+This is the main code folder for running the CRA Toolbox with a Matlab GUI and a model written in SBML Language. It contains the following files:
+
+1. gui_CRA.m is the function for starting the main GUI. It contains all the functions of the elements in the main GUI.
+   It recalls the following functions:
+   1.1 start_simulation.m: function that executes the CRA algorithm.
+2. gui_CRA.fig is the figure of the graphical interface defined in gui_CRA.m. It allows us to specify the following parameters for
+   performing the CRA:
+   - stop time of the simulation;
+   - type of ode solver and step of the time vector;
+   - number of independent realizations of the procedure to perform;
+   - lower and upper boundaries of the Latin Hypercube to generate;
+   - number of samples of the Latin Hypercube;
+   - variable of the model to set as reference node to measure.
+3. gui_MIRI.m is the function for starting the second GUI for computing MIRI. It contains all the callbacks of the elements in the GUI. 
+   It recalls the following functions:
+   3.1 compute_MIRI.m: function that computes MIRI of the model parameters with respect to the chosen output variable
+   3.2 plotpdf_param.m: function for visualizing the conditional probability density function (pdf) of all 
+   the model parameters.
+4. gui_MIRI.fig is the figure of the graphical interface defined in gui_MIRI.m. It allows us to specify the following parameters for 
+   computing MIRI of the output node selected in the previous GUI:
+   - type of evaluation function. It is possible to choose among three evaluation functions: area under the curve, maximum value and time 
+     of maximum of the time behavior of the chosen variable;
+   - number of samples N to include in the upper and lower tail of the evaluation function pdf;
+   - method for computing the tails of the evaluation function pdf. It is possible to choose between two methods: sort and tmp_sum. 
+     The sort method orders all the samples of the evaluation function and selects the N lowest and highest values.
+     The tmp_sum method calculates the lower and upper quartile of the pdf, computing the threshold values in an adaptive manner.
+     The initial lower threshold is set to 0 and it is repeatedly increased of the step size defined by the user until at least N samples 
+     are included in the tail. The same procedure is repeated for the upper tail, starting from a threshold equal to 1. 
+5. start_simulation.m is the function executed when the button START SIMULATION in the main GUI is pushed. It takes in input 
+   the handles of the main GUI in order to retrieve all the variables inserted by the user. For each independent realization, 
+   it generates the Latin Hypercube and simulates the model.
+6. compute_MIRI.m is the function executed when the button COMPUTE MIRI in the second GUI (gui_MIRI) is pushed. It takes in input 
+   the handles of both GUIs and it computes MIRI of the selected variable. It plots boxplot of MIRI values and the pdf of the
+   evaluation function of the chosen variable. It saves MIRI values and the pdfs of both the evaluation function and parameters of the model.
+   It also generates the histogram of the evaluation function.
+7. plotpdf_evalfunc.m is the function that plots and saves the estimated pdf of the evaluation function for the chosen output node.
+8. plotpdf_param.m is the function that plots and saves the conditional pdfs of model parameters.
+
+
+The folder Classes contains the following classes necessary for running the CRA Toolbox:
+
+ 1. EvaluationFunction.m is the abstract class for a generic evaluation function.
+ 2. Area.m is a concrete class that extends the abstract class EvaluationFunction. It computes the area under the curve of a 
+   model variable.
+ 3. Maximum.m is a concrete class that extends the abstract class EvaluationFunction. It computes the maximum value of a variable curve
+ 4. TimeOfMaximum.m is a concrete class that extends the abstract class EvaluationFunction. It computes the maximum point value of 
+    a variable curve.
+ 5. TailMethod.m is the abstract class for defining a generic method that computes upper and lower tails of a parameter pdf. 
+    The upper tail is conditioned to high values of the evaluation function while the lower tail is conditioned to low values 
+    of the evaluation function. 
+ 6. sorted.m is a concrete class that extends the abstract class TailMethod.
+ 7. tmp_sum.m is a concrete class that extends the abstract class TailMethod.
+ 8. TimeBehavior.m is the class representing the time behavior of a model variable.
+ 9. LatinHypercube.m is the class representing the Latin Hypercube generated for perturbing the parameter space.
+10. pdfEstimator.m is the class representing an object for estimating a probability density function through the method ksdensity
+11. MIRI.m is the class for computing the Moment Independent Robustness Indicator (MIRI) of each model parameter   
+
+The folder Examples contains some ODE models in SBML format:  
+- PulseGenerator.xml 
+- EGFR_IG1FRmodel.xml
+- model_Peng2016_reduced.xml